Honestly, even after spending plenty of free time studying narratology the best an amateur can without paying money, I'm not sure I even have the firmest grasp on what defines a beginning, a middle, and an end in any story.

From what I can understand, beginning introduces everything that is mundane and known to a focal character. Something new happens, the focal character tries to fix things their usual way, leading to a "no turning back" scenario, i.e. the middle. A question is presented that is answered in the end.

The middle introduces stuff the focal character is unfamiliar with and consists of dynamic interactions between old and new elements. Stuff gets worse despite the focal character's best efforts.

The end is where new elements are no longer introduced, the conflict is resolved, and the question from the beginning is answered. The aftermath is also shown.

Do I have the basic structure down? And am I misguided for trying to adhere to this structure in the first place?

You could definitely apply that logic to certain SCP articles. On the whole, though, I would say that the logic here isn't really presented, at least not through a very recognizable lens. Due to the nature of them, the individual SCP article doesn'treally have a 'protaganist' that has the mundane, the normal as a baseline. It doesn't have much of a 'new' thing happen to them to make them question the normal or try and return to that normal.

The 'middle' is oftentimes presented towards the end of SCP articles. It is the Foundation's attempts at containing the situation and preventing things from getting worse.

Sometimes that middle has a resolution. Sometimes it doesn't. Sometimes its something in between.

I think though, where things get interesting, is if you look at the SCP articles as being connected. While there isn't really any way to connect all of them to the same universe, you can certainly connect a large amount of the articles onsite to the same universe. When you do that, the baseline of normalcy becomes present. You see the amount of shit the Foundation has to deal with on a daily basis and the lengths they go to in order to reach their goal of containment.

While the method of thinking is an interesting way of analyzing the wiki as a story, I believe that adhering to that narrative theory is ultimately limiting, at the very least with regards to contributing to the wiki. While it isn't misguided, forming just a very basic outline of how any story works isn't the best way of coming up with a story of your own. Feel free to break free from any of these general rues, as often, those are where the most interesting stories are to be had.